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  1. Jalview
  2. JAL-3750

Can't open file from https:// when headless

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    Details

    • Type: Bug
    • Status: Open
    • Priority: Major
    • Resolution: Unresolved
    • Affects Version/s: None
    • Fix Version/s: 2.11.1.1
    • Component/s: Command Line Interface
    • Labels:
      None

      Description

      Jalview reports 'Can't find https:...' when -headless used and it is asked to open a url with protocol other than http://

      (base) ls30857-3:jalview jprocter$ jalview -headless -open https://www.jalview.org/examples/uniref50.fa
      Running jalview.bin.Jalview with -Xmx15461881856
      Java version: 12
      Java Home: /Library/Java/JavaVirtualMachines/adoptopenjdk-12.jdk/Contents/Home
      x86_64 Mac OS X 10.13.6
      Jalview Version: 2.11.1.0 (bioconda (build 0) git-commit: [])
      Quaqua LaF not available on this plaform. Using VAqua(4).
      See https://issues.jalview.org/browse/JAL-2976
      Ignoring SO:0001957 as obsolete and duplicated by SO:0001979
      Ignoring SO:0000437 as obsolete and duplicated by SO:0000800
      Ignoring SO:0000554 as obsolete and duplicated by SO:0000801
      Ignoring SO:0000767 as obsolete and duplicated by SO:0000179
      Ignoring SO:0000058 as obsolete and duplicated by SO:0000803
      Ignoring SO:0001052 as obsolete and duplicated by SO:0001649
      Ignoring SO:0000052 as obsolete and duplicated by SO:0000802
      Ignoring SO:0001053 as obsolete and duplicated by SO:0001648
      Loaded Sequence Ontology from so-xp-simple.obo.zip (199ms)
      CMD [-open https://www.jalview.org/examples/uniref50.fa] executed successfully!
      Can't find https://www.jalview.org/examples/uniref50.fa

      But:
      (base) ls30857-3:jalview jprocter$ curl https://www.jalview.org/examples/uniref50.fa
      >FER_CAPAA Ferredoxin
      -----------------------------------------------------------ASYKVKLITPDGP
      IEFDCPDDVYILDQAEEAGHDLPYSCRAGSCSSCAGKIAGGAVDQTDGNFLDDDQLEEGWVLTCVAYPQSDV

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            Assignee:
            jprocter Jim Procter
            Reporter:
            jprocter Jim Procter
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              Dates

              Created:
              Updated: